What's New on the GeneCards site
Update to Version 3.12: 14 Sep 2014 Previous version User Views
- MalaCards: Synchronized with MalaCards Version 1.06, including improved disease-gene mappings.
- GeneAnalytics: Synchronized with GeneAnalytics Version 1.0
- GenesLikeMe: Now fully integrated into the webcard
- PharmGKB: Updated compounds
- Addgene: New provider of plasmids (see AAK1)
- eBioscience: New provider of proteins, ELISAs, and Flow cytometry products (see IL6 and FGF2)
- ESI BIO: New Cell Lines and PureStem Progenitor Cells (see NANOG)
- 169,579 Entries, 38,656 HGNC approved, 23,282 Protein coding, 123,309 RNA genes
- Introduction of GeneCards Plus, integrated with the LifeMap Network, incorporating:
- GeneALaCart: revamped user interface, offering a clean design and the capability to receive a complete quota's worth of gene details in one batch query.
- VarElect: new next generation sequencing Variant Election facility, which finds and ranks genes related to user-specified phenotype terms.
- GeneAnalytics: LifeMap's powerful and easy to use gene set analysis tool
- PathCards: new pathway-centric site, which unifies human biological pathways consolidated from 12 sources into SuperPaths, based on gene-content similarity.
- GenesLikeMe: formerly GeneDecks Partner Hunter
- GeneLoc: Gene locator, presenting an integrated map for each human chromosome
- COMPARTMENTS Subcellular localizaton database: New protein subcellular localization images with evidence and confidence scores, featured in a new Localization section, along with information from UniProt and Gene Ontology (see CRK)
- HOMER: New Transcription Factor Regulatory Elements motif viewer and Consensus sequence (see CREB1)
- NextProt New ubiquitination and glycosylation sites (see VWF)
- Human Cytochrome P450 Allele Nomenclature Database: New links to CYP alleles and their associated effects (see POR)
- MOPED: Addition of 23 tissues (see POLE)
- Publications: Addition of Journal to article listings (see TPI1)
- QIAGEN: Rebranding and consolidation with SABiosciences
- LifeMap Discovery: Improved presentation of signals and growth factors, organized according to tissues (see TGFB1)
- ApexBio: New compounds (see ARAF)
- GeneALaCart: pre-release, including revamped user interface, offering a clean design, integration with LifeMap Discovery registration, and the capability to receive a complete quota's worth of gene details in one batch query.
- genOway: New source for custom mouse knock-out and knock-in products (see HOXB7) in the Function and Products sections
- LifeMap Discovery: updated data to be in sync with release 1.5, and cosmetic changes to display of datasets
- HGNC: updated URLs
- GenomeRNAi: updated URLs
- 122,658 Entries, 37,730 of them with symbols approved by the HUGO gene nomenclature committee
- Revamped disease-gene list, with links to MalaCards
- GeneCards-generated summaries, with highlights of associated diseases, pathways, and GO terms (see APP)
- IUPHAR: New source for ligands and protein families (see DRD2 and TGFBR3) in the Drugs/Compounds and Domains/Families sections
- MAXQB: New provider of protein expression information (see TLE1)
- UniProtKB: Information about human polymorphisms and disease mutations (humsavar, see FGA) in the Genomic Variants section
- HGNC: Gene families (see LARS) in the Domains/Families section
- LSBIO: New antibodies provider (see SRPX2)
- NONCODE: New links to the database of noncoding RNAs, in the Aliases section (see DLEU2)
- KENES: New showcasing of gene-relevant scientific conferences, in the banner (see PSEN1), Disorders (see FGA), and Transcripts (see MAPK3) sections
- DGV: Improved annotation for structural variations (see APP) in the Genomic Variants section
- LifeMap Discovery: Improved presentation of expression in embryonic tissues and stem cells (see FGF2), in the Expression section
- Sino Biological: New pathways (see AKT1) in the Pathways section, and new lysates (see YES1) in the Proteins section
- Sirion: New premade adenovirus for gene overexpression or knockdown products (see MET), in the Function section
- GeneALaCart: Support for phyla in the Orthologs section
- GEN: Since October, links to Trendy Genes articles at Genetic Engineering & Biotechnology News, from the GeneCards home page
- inGenious Targeting Laboratory (iTL): New source for custom mouse models (see PRKACA) in the Function and Products sections
- Sirion Biotech: New source for shRNA, gene editing, and cell lines (see TNF) in the Function, Transcripts, and Products sections
- Abcam: Updated data
- Expression and RNA images: The HTML rendering has been replaced by actual images; Illumina BodyMap HIMAP values are now shown as the maximal possible value instead of as 0
- GeneDecks: Support for super-pathways
- GeneALaCart: Support for interactions
- 113,522 Entries, 34,080 of them with symbols approved by the HUGO gene nomenclature committee.
- New Unified GeneCards Pathways: GeneCards now clusters all pathways from all sources into super-pathways, based on overlapping gene-sets. Individual genes now portray the relevant super-pathways and their members, in addition to source-based pathway lists (see HK2)
- BioSystems: New source for pathways (see PIK3CA)
- BitterDB: New source, for bitter compounds (see TAS2R38)
- Protein Expression: New integrated protein expression images, incorporating data from MOPED and new source PaxDB (see TBXAS1 and algorithm description)
- RNA Expression: Restoration of links to GeneAnnot (see RASA1)
- SNPs: Addition of Clinical Significance column (see INSR)
- Orthologs: New link to TreeFam gene tree (see CD4)
- LifeMap Discovery™: New summary in the Function section, incorporating embryonic development secreted signals and signal effects, and growth-factor-related stem cell differentiation protocols (see BMP2); also, improved cultured and protocol-derived cells associated with stem cell differentiation in the Expression section (see CTSK)
- Vector BioLabs: New provider for clones, in the Function, Transcripts, and Products sections (see MSH2)
- Utopia: New collaboration, featuring dynamic links to GeneCards information via their customized PDF reader for published articles (see S100B)
- Origene: New custom services, in the Proteins, Function, Transcripts, and Products sections (see USP7)
- Abcam: Epitomics is now an Abcam company, and has been re-branded in the Proteins and Products sections (see IGF1)
- CenterWatch: New links to drugs and clinical trials (see LPL)
- GeneALaCart: Support for BioSystems pathways, and secondary UniProt protein accessions.
- 122,413 Entries, 33,553 of them with symbols approved by the HUGO gene nomenclature committee.
- Gene Expression images: New RNA-Seq data from Illumina BodyMap, expanded 76 tissue repertoire from BioGPS, streamlined visualization (see CKM)
- LifeMap Discovery™: New expression data, in embryonic development context (see H19)
- RNA genes: ncRNA cluster graphics (see MEG3), subcategories (see SNORD116-4), and quality scores (see FTX)
- GenomeRNAi: New human phenotypes in the Function section (see IP6K3)
- Disorders: New diseases from MalaCards, our integrated database of human maladies (see GFRA3); new disease links and relevance scores from the DISEASES database (see CRTAP)
- miRTarBase: miRNA-mRNA targeting information (see TET1 and MIR100)
- Genevestigator: Added source for gene expression links (see HAO2)
- LifeMap BioReagents™: New provider, with links to human stem and progenitor cell reagents (see ALPL)
- Thermo Fisher Scientific: New provider of antibodies (see GGTLC1)
- R&D Systems: New pathways (see TGFBR1), secondary antibodies (see FOXP3), and more assays (see PARK2)
- Qiagen: New pathways (see PPARGC1A)
- SABiosciences: New qBiomarker copy number PCR Arrays (see ERBB3)
- GeneALaCart: Support for MalaCards diseases, Qiagen and R&D Systems pathways, and Ensembl transcripts.
- GeneNote and GeneAnnot: Replaced by our new gene expression data and visualizations.
- Introducing MalaCards alpha - an integrated database of human maladies and their annotations, modeled on the architecture and richness of GeneCards, and leveraging GeneDecks and GeneNote. We welcome your feedback.
- 94,514 Entries, 32,990 of them with symbols approved by the HUGO gene nomenclature committee.
- New RNA Genes via new source fRNAdb and GeneLoc, and improved annotation for previously included RNA genes: GeneCards now includes >50,000 RNA genes, a more than three-fold increase over previous versions, with new annotations in the Aliases and Descriptions (see DLEU1), Summaries (see APC), Genomic Views (see ATXN8OS), and Transcripts (see APOB) sections (see algorithm description).
- Reactome: New source for pathways in the Pathways and Interactions section (see DLG4), and new links to Protein pages in the Proteins section (see KCNK18).
- GeneGo(Thomson Reuters): New source for pathways in the Pathways and Interactions section (see CYP1A1).
- PharmGKB: New and improved listings in the Summaries (see CYP2C19), Pathways and Interactions (see ABCB1), Drugs and Compounds (see CYP2C19), and Specialized Databases (see BPIFB6).
- SIMAP: New source for protein-based similar genes, in the Paralogs section (see CDR2).
- DISEASES: New source for Gene/Disease relationships, in the Disorders and Diseases section (see TP63).
- MOPED: Improved protein expression graphs, now encompassing 14 tissues (normal, cancer, cell lines), in the Proteins section (see GANAB).
- Pseudogenes.org: Improved links to related pseudogenes, in the Paralogs section (see KIR3DX1).
- Advanced Search: New capability to upload a subset of genes along with query terms, enabling gene prioritization within results.
- SwitchGear Genomics: New product provider for 3'UTR and Promoter plasmids, in the Genomic Views (see DGKK), Function (see OSGEPL1), Transcripts (see GRPEL1), and Products (see PLEKHH1) sections.
- Qiagen: New QuantiTect SYBR Green Assays in the Transcripts and Expression sections (see MBOAT2), and new mouse and rat products in the Genomic Views (see FAM134A), Function (see AFF4), Transcripts (see MOB3C), Expression (see FBXL6), Genomic Variants, and Products (see KRT32) sections.
- SABiosciences: New mouse and rat products, in the Pathways and Interactions (see ARNT), Transcripts (see NPR2), and Expression (see SORCS3) sections.
- EMD Millipore: New mouse and rat antibodies, in the Proteins section (see EIF4EBP1).
- OriGene: New mouse and rat products, in the Function (see LAMA3), Transcripts (see PKD1L2), and Expression (see PNMA1) sections.
- USCN: New recombinant proteins and antibodies, in the Proteins section (see THUMPD2).
- GeneALaCart: Contigs have been added to the Genomic Views section, GeneGo(Thomson Reuters), Reactome, and PharmGKB pathways have been added to the Pathways and Interactions section, and DISEASES disorders have been added to the Disorders section.
- BioTime and Subsidiary LifeMap Sciences Announce Agreement to Acquire XenneX, Inc.
- Advanced Cell Diagnostics, Inc. (ACD): New provider for new product type, RNA in situ hybridization assays (see A2M), with links in the Function, Expression, and Products sections.
- BioTime: New ESI hES cell lines (see DPPA4) in the Function section.
- 68,445 Entries, 32,088 of them with symbols approved by the HUGO gene nomenclature committee.
- Ensembl Pan Taxonomic Compara: Orthologs from non-eukaryotic domains were added including 1 archea (Pyrococcus horikoshii) and 5 bacteria (Escherichia coli, Mycobacterium tuberculosis, Streptococcus pneumoniae, Wolbachia pipientis, and Neisseria meningitidis) (see ABCA7) in the Orthologs section.
- STRING: New Interaction Network Preview image (see WIPF1) in the Pathways and Interactions section.
- MGI: New direct listing for mouse knockouts (see KLRK1) in the Function section.
- BioTime: New provider, with links to Cell Lines (see LEPR) in the Function section.
- DNA2.0: New provider of custom synthetic genes, with links to Protein Engineering (see PRKCQ), Gene Synthesis (see TNFSF11), and Variant Synthesis (see ALDH7A1), in the Function, Transcripts, and Genomic Variants sections.
- EMD Millipore: New links to Small Molecules (see PIK3C2A) in the Drugs and Compounds section.
- Sigma-Aldrich: New links to ELISAs (see CAMP) and Cell Lines (see TP53) in the Proteins and Function sections.
- QIAGEN: New links to QuantiFast Probe-based Assays (see CD72) in the Transcripts and Expression sections.
- Tocris Bioscience: New links to Pathways (see NOS3) in the Pathways and Interactions section.
- GeneALaCart: SABiosciences microRNAs and bound targets have been added to the Function section, Tocris and SABiosciences have been added to the Pathways and Interactions section, Ensembl pan taxonomic compara has been added to the Orthologs section, and SABiosciences has been added to the Genomic Variants section.
- 67,217 Entries, 30,345 of them with symbols approved by the HUGO gene nomenclature committee.
- SPIRE MOPED: New Protein Expression graphs (see ANXA4) in the Proteins section.
- DME: New Specific Peptides (see PGD) and additional EC numbers (see HIBADH) in the Proteins, Aliases, and Gene Function sections. from the University of Tel Aviv's Data mining of Enzymes project.
- Ensembl Pan Taxonomic Compara: Orthologs for additional species including opossum, platypus, lizard, sea urchin, honey bee, trichoplax, sea anemone, a chromalveolate, a filamentous fungus, stem rust fungus, and moss (see ALG11)
- HMDB: New listings for compounds associated with a particular gene (see CMAS) in the Drugs and Compounds section.
- DrugBank: New listings for drugs associated with a particular gene (see GSTM1) in the Drugs and Compounds section.
- TarThera: New listings for drugs (see KDR) and diseases (see TP53) associated with a particular gene in the Drugs and Compounds and Disorders sections.
- I2D: Additional protein-protein interactions from the Interologous Interaction Database (see GRM1) in the Pathways and Interactions section.
- SABiosciences: New Bound Targets (see STAT1) and Cancer Mutation PCR Arrays and Assays (see NRAS), and improved Expression PCR Arrays (see HSP90AB1) and Pathway-Focused PCR Arrays (see TNF) in the Gene Function, Genomic Variants, Expression, and Pathways and Interactions sections.
- GeneALaCart: Tocris, HMDB, DrugBank, PharmGKB, and TarThera have been added to the Drugs and Compounds section. PharmGKB and TarThera have been added to the Disorders section.
- 67,398 Entries, 30,105 of them with symbols approved by the HUGO gene nomenclature committee.
- Qiagen: New service provider, with links to Pyrosequencing Assays (see MMP17), siRNA (see ABHD8), microRNA (see FLAD1), and PCR Resequencing Primers (see UBR2) in the Genomic Views, Gene Function, Transcripts, Genomic Variants, and Products sections.
- GenScript: New service provider, with links to Recombinant Proteins (see SRC), Antibodies (see TEC), Assays (see ACE2), Clones (see SLC2A14), and Cell Lines (see ADORA3) in the Proteins, Gene Function, Transcripts, and Products sections. When products are not available, there are links to order custom products (see AAA1). A new banner featuring GenScript products has been added.
- USCN: New service provider, with links to ELISAs in the Proteins and Products sections (see ATP2B3).
- Origene: New product types: immunoassays (see PDGFA), fluorogenic cell assays (see CASP3), miRNA primers (see MIRLET7A1), 3'UTR clones (see NYNRIN), microRNA expression plasmids (see MIR100) in the Proteins, Expression, Transcripts, and Products sections.
- Sigma-Aldrich: New links to microRNA target validation systems (see BRD7) in the Transcripts and Products sections, and to CompoZr Knockout ZFN (see TP53) in the Function and Products sections.
- SABiosciences: New PCR arrays (see KCNS3) in the Pathways, Expression, and Products sections.
- neXtProt: New links to this initial offering of a planned comprehensive human-centric discovery platform, in the Proteins section (see DHX30).
- GeneALaCart: Allele frequencies and sample size are now available in the Gene Variants section.
- Improved explanation of Relevance Scores in search results.
- New Site Map.
- 67,425 Entries, 29,587 of them with symbols approved by the HUGO gene nomenclature committee.
- ProSpec: New service provider, with links to recombinant proteins in the Proteins section (see ADIPOQ).
- SABiosciences: New shRNA (see CXCR3). A new banner featuring SABiosciences products has been added.
- Sigma-Aldrich: New links to Molecular Interaction Network (see EGFR).
- Origene: New product types: siRNA (see A4GALT) and lysates (see PPP1CC).
- UCSC: New links to transcripts (see TP53).
- Search Results: Sort option was added to Symbol, Category, GIFtS and Score (see C-termini).
- Exporting search results gene lists: New links to set analysis tools at the University of Nottingham- TopoGSA and EnrichNet (see tremor).
- Improved User Guide
- Advanced Search: The Advanced search has been improved greatly and it is now out of alpha.
- GeneDecks: Improved performance (see GeneDecks).
- GeneALaCart: Large batch results (over 250 genes) can now be sent via email. "Select all" buttons were added where relevant.
- 68,399 Entries, 29,056 of them with symbols approved by the HUGO gene nomenclature committee.
- Database of Genomic Variants (DGV) New data on structural variations from DGV, including copy number variations, insertions/deletions, and inversions (see ERC2).
- Intellectual Property and GeneIP: The Licensable Technologies section has been renamed Intellectual Property. In addition to licensable technologies, it also includes a link to GeneIP and news items relating to GeneCards and IP (see CCR5).
- Sino Biological: New service provider, with links to proteins (see ACE2) and clones (see AAMP) in the Proteins, Gene Function, and Services sections.
- SABiosciences: Chromatin IP primers and methylation primers (see EDEM1), microRNAs and RNA related products (see PTK2B), and RT2 qPCR primers (see new primer sub-section of RFK).
- Origene: New product types: SYBR primers (see AIRE), shRNA RFP and basic RS shRNA (see BDH1), and antibodies (see ITGB2). A new banner featuring Origene products has been added.
- Novus: New proteins and lysates (see RXRB).
- Abnova: New HuPro® proteins (see MMP3).
- STRING: Interactions are now sorted by database and experimental scores (see RELB) and algorithm description.
- GeneDecks Improvements: Set Distiller now supports expression patterns. Paralog Hunter is faster now, and has been renamed to Partner Hunter.
- GeneALaCart Improvements: The UniProt Recommended Name has been added to the Proteins section. Aliases and Descriptions have been unified to match the GeneCards display. The Expression section now includes probesets from U133.
- Retiring of Version 2: Version 2 has now been frozen (V2.42 data is from Feb, 2010).
- 73,017 Entries, 28,656 of them with symbols approved by the HUGO gene nomenclature committee.
- Version 3: GeneCards V3, with its improved search engine and enhanced GeneDecks, is now the default live version. We welcome your feedback.
- GeneDecks: GeneDecksing, via V3 Paralog Hunting, is now newly available from the card for ontologies (see PGR), phenotypes (see CD19), drugs and compounds (see IGF2R), sequence-based paralogs (see NFKB1), and disorders (see RGS3), and improved for pathways (see MAPK3), binary patterns (see ZIK1), and domains (see RAB32).
- Applied Biosystems: New support for AB GeneAssist pathways in the cards, (see MAPK9), GeneDecks and GeneALaCart. A new banner featuring AB products has been added.
- Pathways Images: Pathways are now showcased via new small generic images, to give one a sense of what is shown after clicking on the actual pathway links. These images are currently supplied for Millipore, Sigma-Aldrich, Applied Biosystems, and Cell Signalling Technologies pathways. See BAX.
- Epitomics: New antibody supplier. Products from Epitomics are now featured in the Proteins and Services sections. See MYC.
- Tocris: New gene summary information, in the card's Summaries section, and in GeneALaCart. See DRD4.
- LSDB: New links to the Human Genome Variation Society's Locus Specific Mutation Databases, in the disorders section. See ACHE.
- Sigma-Aldrich: New product types: Elisa assays (see TP53) in the Proteins section, and new iPSC Reprogramming Factors (see SOX2) in the Gene Function section.
- Aliases and descriptions: Improved unified presentation; the official description is now shown first, followed by a ranked list of the gene's aliases and descriptions, ranked according to the number of GeneCards sources that associate the alias/description with the gene. External identifiers are now shown under the merged alias/description list. See FHIT.
- GeneALaCart: New summaries section, featuring summaries from Entrez Gene, Uniprot, and Tocris. New support for AB pathways. New option in the Orthologs section to request only organisms of choice.
- Sigma-Aldrich: New support for "Your Favorite Gene" pathways in GeneCards, GeneDecks, GeneALaCart, and V3. See MAPK3; new siRNA, shRNA and esiRNA products in the Function, Transcripts, and Services sections.
- SABiosciences: New links to its transcription factor binding sites, and to its interacting genes and proteins networks. See FUT1 and ACHE respectively.
- OriGene: New human purified proteins. See MSTN.
- BGMUT: New links to the Blood Group Antigen Gene Mutations database in the Disorders and Mutations section. See ABO.
- Enzo Life Sciences: Biomol has been acquired by Enzo Lifes Sciences, so all relevant links have been renamed accordingly. See PDGFRB.
- Publications: Two new papers, about GeneDecks and GIFtS, have been accepted for publication. See Our Publications.
- Streamlined presentation of product data in the Function and Transcripts sections.
- New mirror site at the Bioinformatics Institute of A*Star in Singapore.
- Version 3: Improved GeneCards searches and GeneDecks functionality, including a new option to download GeneDecks results to an Excel file; new availability of V3 for commercial users.
- 55,546 Entries, 28,139 of them with symbols approved by the HUGO gene nomenclature committee.
- Millipore: New support for pathways, in GeneCards, GeneDecks, and GeneALaCart. See SERPINA3.
- GeneALaCart: New support for PubMed Ids; more visible External Ids; Millipore pathways
- Origene: New products in the Transcripts and Function sections, including full length, GFP-Tagged-ORF, and MycDDK-Tagged-ORF clones, qPCR primers, and shRNA.
- Cell Signaling Technology (CST): New Sandwich ELISA Kits, in the Proteins section's Assays subsection.
- Novoseek: Renamed from AKS, with new disease and compound links.
- Version 3: Improved searches and wildcard handling; new capability to send search results to GeneDecks's Set Distiller as well as to GeneALaCart or Genomica; bug fixes and performance improvements
- GeneDecks Version 3: Support for weights in Paralog Hunter; bug fixes and performance improvements
- Users can now choose to weight GIFtS by data from proteins, orthologs, and/or publications when querying for the GIFtS value of a specified gene, or when retrieving a list of genes within a specified score range.
- Users can now also receive a list of sources that had no data to contribute to a requested query gene of interest.
- After querying for the GIFtS value of a gene, the resulting score is now depicted visually on the GIFtS distribution graph.
- Introducing GeneCards Version 3 beta. It boasts a new, much faster search engine with paged, unlimited results, and support for field specific queries. There are also new minicards with improved readability. Version 3's infrastructure is based on a relational database, available to commercial users in collaboration with Xennex, Inc.
- Introducing GeneDecks
Version 3 alpha, featuring Paralog hunter and Set distiller.
Paralog hunter finds similar genes for a query gene based on shared annotations.
Set distiller finds shared annotations within a user-defined gene set.
We'd appreciate your feedback.
|Version 2.40:||Released on 15 Feb 2009|
|Version 2.39:||Released on 21 Sep 2008|
|Update 2.38.1:||Released on 25 May 2008|
|Version 2.38:||Released on 17 Feb 2008|
|Version 2.37:||Released on 23 Sep 2007|
|Version 2.36:||Released on 22 Apr 2007|
|Version 2.35:||Released on 05 Nov 2006|
|Update 2.34U1:||Released on 09 Jul 2006|
|Version 2.34:||Released on 02 Apr 2006|
|Version 2.33:||Released on 09 Nov 2005|
|Update 2.32U1:||Released on 05 Sep 2005|
|Version 2.32:||Released on 09 Jun 2005|
|Version 2.31:||Released on 11 Jan 2005|
|Update 2.30U1:||Released on 06 Sep 2004|
|Version 2.30:||Released on 01 Aug 2004|
|Versions 2.29 and earlier:|
Version 2.40: Released on 15 Feb 2009
- 53,264 Entries, 26,391 of them with symbols approved by the HUGO gene nomenclature committee.
- Sigma Aldrich: Expanded functionality, with new links to Human Recombinant Proteins and Small Molecules, in addition to previously featured Antibodies and Antibody Arrays, in the Proteins, Drugs & Compounds, and Services sections. See TNF.
- Novus Biologicals: New Antibodies provider, in the Proteins/Antibodies and Services sections. See RUNX1.
- GIFtS: GeneCards Inferred Functionality Scores are now displayed in the header of each GeneCards gene, in the box containing the symbol, category, and GCid. See examples of genes with high (TP53), medium (ERVK2), and low (DNM1DN9) GIFtS.
- GeneALaCart:GIFtS can now be requested in batch queries, description lists now also contain the gene's main description, and the output of Gene Ontology (GO) information is improved.
- Statistics page: Improved graphs, with nicer colors and removal of obsolete sources.
- Gene Index: Now available at the bottom of each card, in addition to the home page.
- 52,524 Entries, 25,463 of them with symbols approved by the HUGO gene nomenclature committee.
- New Integrated Gene Expression Images: 28 tissues, including cancer tissues as well as normal ones, are now presented in the Expression in Human Tissues section, covering integrated experimental results from GeneNote and the Genomics Institute of the Novartis Research Foundation (GNF) SymAtlas project, as well as electronic Northern and SAGE calculations. Additional new link to GNF BioGPS . See TIMM17B.
- Abnova: New provider, with a variety of targeted offerings, including recombinant proteins, antibodies, chimera RNAi products, in the Proteins, Function, Transcripts, and Services sections. See IGF2.
- Tocris Bioscience: New provider, with compounds, annotated with their actions and chemical abstract registry numbers, in the Drugs and Compounds and Services sections. See EGFR.
- STRING: New source for protein-protein interactions, in the Interacting Proteins table in the Pathways & Interactions section. See AKT1.
- Proteopedia: New link, to the collaborative 3D encyclopedia of proteins and other molecules, for relevant 3D structures in the Proteins section. See LRDD.
- Improved GIFts: GeneCards Inferred Functionality Scores are now based on more sources, displayed on their own page, and available for individual query genes.
- Summaries: New section, featuring descriptions of a gene's function, cellular localization, and effect on phenotype, from EntrezGene, Uniprot and Gene Wiki. See SORT1.
- New links to Gene Wiki in the Summaries section. See PARK2.
- GeneALaCart: Added MGI and SGD to the Similar Genes in Other Organisms section.
- Millipore: New provider, with a variety of targeted offerings, including recombinant proteins, antibodies, kits, assays, clones, and RNAi products, in the Proteins, Function, Transcripts, and Services sections. See IGF2.
- GIFTS: Introducing new GeneCards Inferred Functionality Scores. GIFTS are associated with GeneCards genes as a measure of the level of available annotation detail, used as a predictor for gene functionality. The distribution of inferred functionality scores is available on the Statistics page, where one can view random genes based on selected scores.
- Applied Biosystems: New siRNA products, in the Function and Transcripts sections. See AKT3.
- Abcam: New recombinant protein products, in the Proteins section. See AVPR1A.
- Tufts University: Their technologies that are available for licensing are now featured in the Technologies section. See BRCA2.
- Protein names: Uniprot's recommended protein names are now listed in the Proteins section, in addition to the Aliases and Descriptions section. See CLOCK.
- Categorization: 778 formerly uncategorized genes are now categorized as "protein-coding" due to the existence of an Ensembl protein. See STELLAR.
- GeneALaCart: 1) Support for significantly more detailed Uniprot information, provided in the Protein, Function, and Disorders sections. 2) New Output file order option: in addition to the default behavior of eliminating duplicates, one can choose to instead preserve the exact order of the gene list as specified in the input file and retain duplicates if they exist.
- 46,560 Entries, 24,824 of them with symbols approved by the HUGO gene nomenclature committee.
- Licensable Technologies: New section, featuring, where relevant to particular genes, technologies that are available for licensing. Institutions currently featured include the Weizmann Institute of Science (see AHI1) and the Salk Institute for Biological Studies (see PMCH).
- Sigma-Aldrich: New GeneCards service provider, with Antibodies now available in the Proteins and Services sections. See CCL2.
- R&D Systems: New GeneCards service provider, with Human Recombinant Proteins, Antibodies, and Assays now available in the Proteins and Services sections. See AKT1.
- GeneALaCart: Support for categories, gene description, source, HGNC approval status, cytogenetic band, Refseq and Ensembl protein identifiers, drugs/compounds from almaKnowledgeServer, and orthologs from euGenes.
- Merged User Feedback and survey forms: Surveys will no longer pop up automatically. To contact us, click on the User feedback link at the top of any GeneCards page, and fill out the short form (we value your input!). To compensate for your time, we will conduct another iPod raffle.
- Non-Coding RNAs (ncrnas) in the Transcripts section:
- - New links to RNAdb. (see BCMS).
- - Detailed annotation about ncrnas from Ensembl (see ENSG00000201407).
- Categorization: Improved algorithms, resulting in fewer genes being erroneously marked as "protein-coding".
- OMIM: Links to more disorders, due to improved parsing of their data.
- Human Genome Epidemiology Network (HuGENet, formerly GDPInfo): Updated links in the Disorders section (see NFKB1).
- H-Invitational Database (H-Inv DB): New links in the Other Human Genome Wide Resources section (see MAPK3).
- 46,250 Entries, 24,422 of them with symbols approved by the HUGO gene nomenclature committee.
- New in GeneALaCart: support for SNPs, Paralogs from Ensembl, and Disorders from almaKnowledgeServer. Other improvements include similarity scores in Orthologs, sensitivity and specificity scores for binary patterns, and the capability to query by symbols only (in addition to symbols/aliases).
- Antibodies from GeneTex are now available in the Proteins and Services sections. See A2M.
- Cell based and pathway activation and profiling assays from DiscoveRx are now available in the Gene Function (see ADORA1, MAPK3), Pathways (see AKT1), and Services (see EGFR) sections.
- Bugs have been fixed in the calculation of exonic unit coordinates in the presentation of ASD splice variants. See EYA1.
- Qualifiers have been added to GO terms in the Proteins (see TPX2), Function (see BRCA1), and Pathways (see BRSK1) sections.
- Links to the HUGO Gene Nomenclature Committee (HGNC) site have been updated to reflect their move to EBI.
- Deep links to specific Alternative Splicing isoforms are now provided in the Proteins section (see CFTR).
- The text-only version of the full list of GeneCards gene now displays 1 gene per line for easier post-processing.
- GeneNote binary expressions patterns for non-differentially expressed probesets have been improved. See ABCF3.
- Links to Wikipedia in the Specialized Databases section (see BRCA2), for those genes that Uniprot identifies as having such entries.
- Search results can now be sent to Genomica. For example, after searching GeneCards for hepatitis, click on the Genomica button for further analysis and visualization of the found set of genes.
- 48,383 Entries, 24,158 of them with symbols approved by the HUGO gene nomenclature committee.
- Proteins, assays, and drugs from BIOMOL are now available in the Proteins, Drugs & Compounds, and Services sections. See NOS1.
- New GeneDecks summary tables now rank the degree of similarity, taking into account all shared annotation combinations. Try GeneDecksing ABL1 for pathways.
- New in GeneALaCart: support for Paralogs (HomoloGene) and Transcripts sections (RefSeq and Unigene identifiers), and HGNC ids in Other Genome Wide Resources section.
- GeneALaCart now accepts aliases and HGNC ids as input when using the mixed identifiers option.
- GeneALaCart can now be accessed directly, via the URL: GeneALaCart.
- Default output file for GeneAlaCart is now in MS Excel format (.xls).
- Searching by HGNC id is now possible when using the search by external id feature from the home page or advanced search. To link to a specific GeneCard using the HGNC id, see Linking to Particular GeneCards.
- Links to Ensembl transcript reports with schematic representions were added to the Transcripts section. See LAMA1.
- Links to Ensembl Gene Trees were added to the Orthologs section. See ASL.
- Link to GeneLoc's exon details has been added to the Location section. See AGPAT2.
- Link to the previous GeneCards version has been added to the homepage.
- The user feedback form (from User Feedback link in the orange bar, above) now has a verification step to prevent spam.
- Link to new GeneNote microarray integrated expression images in Expression section.
- 49,002 Entries, 23,864 of them with symbols approved by the HUGO gene nomenclature committee.
- Improved Invitrogen links in Proteins for Human Recombinant Proteins and Antibodies,
and a new link for Assays.
New Invitrogen links in Gene Function for Clones and Primers.
Additional Invitrogen links in Services: Clones, Proteins/Assays/Screening Services, Primers, and for searching the catalog for gene related products. See BTK.
- GeneDecks, now with a preliminary homepage, is also available for CST and Invitrogen pathways, as well as for InterPro domains. See ATM.
- GeneALaCart, with an improved display, now allows download of Invitrogen and CST pathways in "Pathways & Interactions".
- A text box for the output text file name has also been added to GeneALACart.
- Advanced search, including capabilities to refine queries to search only within specific categories or symbols/identifiers, to easily retrieve/edit the specific symbols found after doing a search, and to submit these symbols to GeneALaCart for batch query processing. See Options for further analyzing your results after searching for tay sachs
- SNP location types were added from PupaSuite, including information about SNPs that affect splicing sites, transcription factor binding sites, exonic splicing enhancers and triplexes. Click on the magnifying glass in the Transcription Data column for the first snp in ABCB1.
- Links to HapMap were added to SNPs. See WNT1.
- Improved GO annotations, including evidence codes and links to relevant Pubmed articles
- Pubmed ids were added to article references in Research Articles. See FYN.
- New GeneCards Guide, with explanations and examples of the different features in GeneCards, including a Getting Started, section, designed to help new users.
- RNAi products and Pathways are now available from Invitrogen. In addition, GeneCards also has links to Invitrogen's Antibodies Central, Drug Discovery Central, Human Recombinant Kinases, and Custom Antibody and Peptide Service. See TP53.
- Clones from OriGene were added in the Transcripts and Services section. See UBE2C.
- Search terms, including those for authors, will now be appended to the top ten list for literature and almaKnowledgeServer (AKS) (formerly Bioalma) diseases. See BRMS1, with search term "RhoGDI2" and OLFR@, with search term "Lancet D".
- Specific genes can now be displayed by entering UniProt, Ensembl, or Entrez Gene id into the url using id=<accession>. An optional type (uniprot, entrezgene, or ensembl) can be added for specificity by appending &id_type=<type> to the url. To see the GeneCard for OMD via its Entrez Gene id 4958, use carddisp.pl?id=4958&id_type=entrezgene.
- GeneALaCart can also take the above accessions as input when the "Gene symbols and other identifiers" option is chosen before submitting.
- Accessions from HGNC, EntrezGene, UniProt, and Ensembl are now shown in the Aliases and Descriptions box (as External Ids), with links to the entries at the specific databases. See MAP3K3.
- PharmGKB disease relationships have been added to the disorders section. See HMGCR.
- List of species to which a gene has no orthologs is now displayed in a popup window. See CTH.
- Papers in the Research Articles box now list their sources using superscripts. See RASGRP3.
- Information from Applied Biosystems, Abcam, and Cell Signaling Technology has been updated.
- 47,546 entries, 22,719 of them with symbols approved by the HUGO gene nomenclature committee.
- Introducing...by popular request: Batch Queries! We present a Beta version of GeneALaCart, with the capability to receive selected annotations for sets of genes. GeneALaCart is currently available free of charge to academic and non-profit institutions, with a default limit of 100 genes per day (unless more are requested).
- Antibodies are now available from Cell Signaling Technology (CST) and/or Abcam, in the Proteins and Services sections. See the GeneCard for FGFR1.
- Protein-protein interactions have been added to the Pathways and Interactions section (previously named Ontologies and Pathways). Interactions from MINT and UniProt, with links to IntAct, are now available, as well as CST signaling pathways. See CBL.
- GeneDecks is now available for binary expression patterns. See LIPA.
- Phosphorylation sites can now be viewed (from the Post-translational subsection of the Protein section) via Phosphosite. An example of this functionality for our sample gene (BTK) is available here
- Genomic locations for RNA genes are now available from miRBase. See MIRN101-1.
- The Expression section now also includes links to EXPOLDB. See AANAT.
- Enzyme EC numbers are now included in the function and aliases sections, with links to IUBMB. See ACACA.
- A new Search Box enables data-driven searches of PubMed, OMIM, or NCBI Bookshelf. Queries can include the current gene's aliases and disorders, the search string that led to this gene, and/or user-specified terms. See GBA, one of the genes returned when searching GeneCards for tay sachs. The search box also features a 'Copy to Clipboard' button that allows the whole query string to be copied to the clipboard for use at other external databases.
- The Aliases and Descriptions section has been reorganized. Aliases are now shown separately from descriptions. A link to the new Search Box has also been added to the section. See TJP2.
- Navigation links have been replaced with a dropdown Jump to section menu that lists each GeneCards section and includes links to the top and bottom of the page. The menu is also available on the left hand side of each section. See KRT19.
- Gene Ontology entries are now divided by parent term. Cellular component terms can now be found in Proteins, molecular function terms in Gene Function, and biological process terms in Pathways and Interactions. See DMGDH.
- 46,671 entries, 21,845 of them with symbols approved by the HUGO gene nomenclature committee.
Introduction of preliminary
features for KEGG pathways. While viewing a particular gene, one can now also
click to see all of the other genes that participate in the same pathway(s).
For example, when viewing the pathways for the gene
on the associated GeneDecks icon
brings up the GeneDecks display of other genes that participate in the selected pathways. (By default,
all of the gene's pathways are initially selected.)
We welcome your feedback as we continue to to develop and expand GeneDecks.
- A new Gene Function section has been added. Annotated information from UniProt and Genatlas have been moved into this section from the Proteins and Database sections. In addition, the MGD database is now mined for phenotypes of mouse orthologs, and a detailed popup table is provided for these phenotypic alleles. For example, see the GeneCard for AADAT.
- Improved SNPs. Pie charts are now provided to highlight allele frequencies. In addition, the order of SNPs presentation can now be refined and/or redefined by user specification of sort priorities according to their fields of choice. For example, see the GeneCard for PRAME.
- Searching PubMed from the literature section can now also include gene aliases and/or the current GeneCards search term, as customized by the user.
- Authors are now included for articles in the literature section, and can be specified in GeneCards search queries.
- Improved handling of searches that use wildcards (*).
- PDF files for all of the GeneCards family publications are now available on the publications page.
- GeneCards has a new url! Look for us at www.genecards.org.
- XML by Function is now available for the version 2.32 data. XML by Resource has also been modified and minor bugs fixed. Please contact firstname.lastname@example.org if you'd like to beta-test this feature.
- 35,401 entries, 20,799 of them with symbols approved by the HUGO gene nomenclature committee.
- Drug compound relationships from PharmGKB, shown in the Drugs and Compounds section (formerly Chemical Compounds). See ABCC2.
- Alternative splicing information from the Alternative Splicing Database (ASD) in the Transcripts (formerly Sequences) section. See COQ3.
- GeneAnnot information now includes three chips: U95, U133, and U133Plus2. Note that U95-A refers to Affymetrix array AV2 (version 2). See CASP4.
- Coordinates for olfactory receptor genes come directly from The Human Olfactory Receptor Data Exploratorium (HORDE). See OR10AH1P
- Link to HGNC from databases section.
- Migration from LocusLink to Entrez Gene.
- New paralog information from HomoloGene and Ensembl. See POM121L1.
- Deep links to all cDNA sequences from AceView, which are sorted by quality. See CAD.
- GeneCards categories have been changed for compatibility with Entrez Gene types. An attribute was added intead of the former 'predicted' categories, which apprears in the top left box in the GeneCard display. See COAS2.
- Sorting options have been added to the keyword search, and some improvements have been made to the search algorithm itself. Most searches will run faster now.
- Allele frequency information from NCBI dbSNP was added to the SNPs section. A summary for expression and allele frequency data is displayed, and the details can be viewed in a pop up page. See ABCB1.
- The GeneCards homepage was reorganized to be clearer and more concise. Statistics on the GeneCards categories are provided with links to a sample card from each category and to the statistics page, which provides a keyword search within each category.
- New background color change for easy identification of mouseovers.
- Improved list of disease related genes. Genes listed now include those from more sources. See the disease list.
- 42901 entries, 20046 of them with symbols approved by the HUGO gene nomenclature committee.
- New links to Applied Biosystems reagents including TaqMan® Gene Expression Assays in the Expression in Human Tissues and Sequences sections, and to TaqMan® Genotyping Assays in the SNPs/Variants section. The expanded Services section also contains links to these assays, as well as to AB's VariantSEQr ™ Resequencing Sets and free SNP selection tool.
- New section for Chemical Compounds according to bioalma.
- New bioalma relationships between GeneCards genes and PubMed articles in the Research Articles section, Chemical Compounds in the new Chemical Compounds section and diseases in the Disorders & Mutations section.
- New orthologies from SGDTM - the Saccharomyces Genome Database for the yeast Saccharomyces cerevisiae, commonly known as baker's or budding yeast, in the Similar Genes in Other Organisms section.
- Improved orthologies from HomoloGene in the Similar Genes in Other Organisms section, based on their new technology that measures %similarity on the amino acids level. (Orthologs for organisms for which this data is not yet available are presented using HomoloGene's older nucleic acid based comparisons).
- New Affymetrix probe-sets in the expression section from the newer human HG-U133 set, provided by GeneTide.
- New GeneCards statistics graphs linked to from the GeneCards home page, containing distributions of the GeneCards sources and gene categories (e.g. genes, RNA genes, and clusters).
- Improved GeneCards display including more compact orthologies and SNPs sections, secondary page remaining on top, and the addition of a new information page that documents what's shown in each section.
- Improved search results display. Prior to the presentation of the minicards, an alphabetized list of the found genes is shown, together with a running indication of the %age of cards processed. Clicking on gene brings up the relevant card in a different window.
- Updated list of publications
- GeneTide and xmlByFunction cards have not yet been updated for 2.31. We appreciate your patience
- GeneCards data can now be displayed in XML by function format. This format has the main card fields in the same order as the regular GeneCards display. Please contact email@example.com if you'd like to beta-test this feature.
- The GeneCards search engine no longer times out on queries that are too general; it now identifies the situation and requests that the user enter a more specific query.
- Miscellaneous URL updates and bug fixes.
- 38,829 entries, 19,614 of them with symbols approved by the HUGO gene nomenclature committee
- Introduction of GeneTide, the Gene Terra Incognita Discovery Endeavor, an automated system for human transcript (mRNAs & ESTs) annotation and elucidation of de-novo genes. New link to GeneTide in the sequences section. See ACE
- New link to the Genomics and Disease Prevention Information System (GDPInfo) in the Disorders and Mutations section, see INSR
- New link to ECgene gene models in the Other Genome Wide Resources section
- Cleaner display for lean genes: GeneCards for genes of the uncategorized, disorder loci and reserved symbols categories now only display fields that contain useful information. For example, see the LeanCard for BAS
- Tissue vector images now contain binary patterns. At most 5 unique binary patterns that reflect the over-expression (in black) and under-expression (in white) in different tissues are shown per gene, with their counts on the left. See hIAN2
- Improved navigation of each GeneCard via links at top and bottom to specific fields of the card
- New gene category for symbols reserved by HUGO for future use, see AACP
- New mirror site at the Korea Institute of Science and Technology Information
- The GeneCards mark is now shown with the ® symbol, to reflect its registration in the U.S. Patent and Trademark Office
- Updated list of publications
- 38,338 entries, 18,232 of them with symbols approved by the HUGO gene nomenclature committee
- Links to pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) in the new Ontologies and Pathways box (GO has been moved to this box)
- New link to the Genetic Association Database (GAD) in the Disorders and Mutations section.
- Links to transcript and alignment information at AceView in the Sequences and Other Genome Wide Resources sections.
- Fewer uncategorized genes with the addition of two new gene categories called "potentially expressed sequence" and "RNA genes". For examples, see LOC132430 and RNU12 respectively.
- Display of alternative locations for genes when two sources give conflicting locations and/or one source gives multiple locations. See DUX1 for example.
- The electronic Northern and SAGE counts have been re-normalized, and are now presented on the same root scale in the same range (0-10000) as the experimental tissue vectors.
- Improved rendering of 3D protein structures via an upgraded
For example, see the PDB id 11RK ( 3D) link in the Proteins section of the INSR gene.
- A revised academic mirror site licensing agreement which also covers GeneNote, GeneAnnot, and GeneLoc in preparation for their eventual availability as mirror packages.
- Updated list of publications
- 53,795 entries, 16,909 of them with symbols approved by the HUGO gene nomenclature committee
- Display of CGAP SAGE tags, as well as graphics for associated tissue vectors
- 2 new columns in the Expression section gene annotation table. Data matches the Correlation (x) and Relative length (y) axes of the GeneNote variation plot
- Inclusion in Domains and Families section of clustering information from Hebrew University's Protonet automatic hierarchical classification of proteins system
- New Related Human Genes box, enumerating associated pseudogenes, with links to pseudogene.org
- New display by GC id option (displaying by GC17P034621 brings up the card for CCL2)
- Wildcard search feature for symbol/alias and GC id options (see microcards for genes whose symbols match BRCA*)
- Chromosomal location section now displays other genes whose exons overlap with those of the presented gene, as determined by GeneLoc
- Updated list of publications
- Updated gene expression tissue vectors and variation plots to reflect upgraded prostate and pancreas experiments
- Ability to view GeneCards genes on a UCSC genome viewer Custom Track
- New mirror site at the Institute of Food Science and Technology - CNR Avellino, Italy
- Announcement of agreement with XenneX Inc to commercialize GeneCards.
- The GeneAnnot website is now live.
- Unified set of logos for GeneCards, GeneLoc, GeneNote and GeneAnnot
- Bug fixes:
- Links to OMIM were not always displayed.
- Variation plots and tissue vectors were not always in sync with respect to the number of probe-sets that were included/excluded.
- Updated XML schema files.
- Updated list of publications.
- 47,794 entries, 16,038 of them with symbols approved by the HUGO gene nomenclature committee.
- Expression section now contains tissue vectors for all genes in the GeneNote project that have been matched to Affymetrix probe-sets via the GeneAnnot system.
- Enumeration of GeneAnnot gene-to-probe-set associations, including probe-set identifiers, arrays (A-E), sensitivity and specificity scores, and counts of the number of genes mapped to particular probe-sets.
- New GeneNote variation plots that depict how associated probe-sets are included/excluded into tissue vector calculations. To be included, associated normalized intensity levels must reach a threshhold (of 10) in at least one tissue. This variation is visualized in the x-y plane: the x-axis shows Pearson's correlations between individual probe-sets vectors and the average tissue vector; the y-axis shows the relative length of an individual probe-set vector (its scalar length divided by that of the average vector).
- Renaming of the Unified Database(UDB) for Genome Mapping to GeneLoc, and release of GeneLoc version 2.7
- Mining and displaying of Orthologies from NCBI's HomoloGene database for pig (Ssc, Sus scrofa), cow (Bt, Bos taurus), rat (Rn, Rattus norvegicus), mouse (Mm, Mus musculus), frog (Xl,Xenopus laevis), zebrafish (Dr, Danio rerio), fly (Dm, Drosophila melanogaster), worm (Cel, Caenorhabditis elegans), tomato (Les, Lycopersicon esculentum), barley (Hv, Hordeum vulgare), rice (Os, Oryza sativa), wheat (Ta, Triticum aestivum), corn (Zm, Zea mays(maize)), thale cress (At, Arabidopsis thaliana), and/or medicago truncatula (Mtr).
- Moving of Swiss-Prot's tissue specificity information to the Expression section.
- Inclusion of additional gene aliases from LocusLink
- Annotation of previous GC identifiers where relevant (in cases that GeneLoc deems it necessary to assign a new identifier to a gene based on updated information about its chromosomal location). Such GC ids will always remain with their original genes and will not be reused with other symbols.
- Elaboration of Gene Ontology (GO) terms to include textual descriptions in addition to GO identifiers.
- UDB now fully incorporates the GeneLoc algorithm
- GeneCards are now printable in landscape mode.
(use Page Setup to choose landscape, A4 paper,
and 0 length right margins - and Print Preview first to verify).
Tested browsers include PC Internet Explorer Versions 5-7, and Netscape Version 7
- Erroneous InterPro links are no longer displayed in the cards. (Any erroneous InterPro or gene description data shown in a mini-card but not in the actual card, and any pseudogene classification based on this erroneous description, should still be ignored - these will be fixed in release 2.27).
- GeneCards data can now be displayed in XML. Please contact firstname.lastname@example.org if you'd like to beta-test this feature.
- 44,738 entries, 15,002 of them with symbols approved by the HUGO gene nomenclature committee.
- Enumeration of all of the genes (the GeneLoc subproject), integrating positional information from LocusLink and Ensembl, assigning integrated gene locations, and unique and meaningful GeneCards identifiers based on these locations. For example, the GC identifier for the BRCA2 gene is GC13P030875 .
- Using the GC numbers, the ability to search GeneCards for genes in a particular region. For example, one can search for GC01P001* to see all the genes on the + strand in the first kilobase of chromosome 1.
- Links to new UDB/GeneLoc gene density information in the Chromosomal Location section. For example, the APP gene links to gene density information for chromosome 21.
- 3385 new cards for novel genes predicted by Ensembl, categorized as predicted genes with support. For example, see the GeneCard for ENSG00000116726.
- Links to GeneOntology information in the Proteins section.
- Links to Leiden Muscular Dystrophy pages when relevant. For example, see the Specialized Databases section in the GeneCard for DMD.
- New expression legends with additional clone count information for electronic Northern tissue vectors.
- New GeneCards publication: Safran et al, 2002, "GeneCards 2002: towards a complete, object-oriented, human gene compendium", Bioinformatics Vol 18 no.11.
- 74,026 entries, 14,659 of them with symbols approved by the HUGO gene nomenclature committee.
- Enriched Expression section (see CFTR), now including figures of the gene's expression in Normal human tissues:
- More orthologies: new fly and worm data mined from euGenes and linked to Flybase and WormBase (see ACTA1).
- New figure of the gene on its chromosome, based on data mined from Ensembl (see APP).
- Better categorization into: genes (e.g. BRCA1), predicted genes (e.g. LOC137904), predicted genes with support (e.g. LOC153619), pseudogenes (e.g. PROSP) clusters (e.g. IGH@), disorder loci (e.g. AD6) and uncategorized cards (e.g. COX7B2), with statistics shown on the home page.
- More aliases and additional descriptions, sorted alphabetically.
- Improved Protein section, now containing protein REFSEQs.
- New "Protein Domains/Families" section, currently linking to InterPro and BLOCKS.
- Improved "SNPs/Variants" section, including a new link to SWISSPROT's variants section and an improved display of the SNP table.
- Improved databases section, with databases now divided into distinct categories: genome wide, general, limited scope, specialized, and services.
- Highlights of some GeneCards algorithms via tooltip balloons.
- Since the last release, three new GeneCards mirror sites: Univ of Texas M.D. Anderson Cancer Center, Houston, TX, USA, Zentrum f?r BioInformatik, University of Tuebingen, Tuebingen, Germany and South African National Bioinformatics Institute (SANBI), University of the Western Cape , Bellville, South Africa.
27 February 02: release of version 2.24
- 72,704 genes and 49 gene clusters, 14,257 of them with symbols approved by the HUGO gene nomenclature committee.
- Expansion of the SNP section to display additional fields about each SNP.
The SNP table is now divided into two sections,
one for genomic data and
the other for transcripts.
The genomic section includes the SNP id, contig accession (NT number),
position in the contig, orientation, nucleotide change, 5' and 3' flanking sequences
and whether or not the SNP has been experimentally validated.
The transcription section lists for each shown transcript, the SNP type
coding, splice-site, mrna-utr, intron, locus-region),
mRNA accession, protein accession, open reading frame, position of the SNP in the protein
and amino acid change. The presented SNPs are sorted first by validation status,
and then by SNP type.
For example, see the SNP section of the BRCA2 GeneCard
- New link to IMGT, the international ImMunoGeneTics database, in the "This Gene in Specialized Databases" section (previously called "Additional Sources of Information on the Web")
- New "Expression in Human Tissues" section, currently linking to SOURCE (The Stanford Online Universal Resource for Clones and ESTs).
- New link to GeneLynx in the "This Gene in Other Gene-Based Resources" section.
- Improved disease genes curation and processing.
26 November 01: release of version 2.23
- 27,612 genes and 51 gene clusters, 13,548 of them with symbols approved by the HUGO gene nomenclature committee.
- Expansion of the SNPs section to display details about selected, not withdrawn, single nucleotide mutations including SNP Id, contig id, contig position, orientation, and nucleotide change, with option to show the complete table of extracted data. For example, see the SNP section of the RUNX1 GeneCard
- Inclusion of gene description information for C. elegans homologs
- Capability to request a random GeneCard from the subset of HUGO approved genes as well as from the entire set of GeneCards genes.
- An alpha version of GeneCards data in XML format (for GeneCards licensees and academic mirror sites).
6 September 01: release of version 2.22
- 29,268 genes and 48 gene clusters, 13,395 of them with symbols approved by the HUGO gene nomenclature committee.
- Links to the Ensembl Database, providing additional annotated information of known human genes in the genome sequence and prediction of additional genes with supporting evidence.
- Direct links to three-dimensional visualization of PDB structures. For example, to see the visualization for the 1olg structure of the TP53 gene, click on the associated 3D link in the Proteins section of the card.
- More complete SNP information.
- Counting of alternative splicing transcripts in the Sequence section of the card.
- Improved algorithm for bringing relevant literature from PubMed.
- Restored and improved access to the clone collection at the Resource center (RZPD), German Human Genome Project.
- Since the last release, two new GeneCards mirror sites: in Torino, Italy at the Dept. of Clinical and Biological Sciences, University of Torino, and in Paris, France at the Curie Institute.
13 June 01: release of version 2.21
- 22,420 genes and 44 gene clusters, 13,046 of them with symbols approved by the HUGO gene nomenclature committee.
- New and improved graphics, developed by DoubleTwist.
- Improved algorithm for linking cards to the UCSC Golden Path.
- Information on C.elegans homologs from the University of Stony Brook C.elegans-H.sapiens Alignment Database, providing a comprehensive source of information about the genetics of worms. GeneCards displays characteristics of the corresponding C.elegans gene, including its symbol, GeneBank accession numbers, and percent of total similarity to the human gene.
- New capability of viewing a random GeneCard from the GeneCards Homepage.
16 Apr 01: release of version 2.20
- 20,417 genes and 41 gene clusters, 12,892 of them with symbols approved by the HUGO gene nomenclature committee.
- New section for Single Nucleotide Polymorphisms (SNPs) according to the NCBI SNP Database. SNP location is hyperlinked in the box if it is in the coding-synonymous, coding-nonsynonymous or splice-site region of the gene. All other SNPs are available via gene-specific links, and their IDs can be used in GeneCards search queries.
- Links to the Weizmann Institute of Science GESTALT Workbench (GEnomic Sequence Total Analysis and Lookup Tool) for analysis of large-scale genomic sequence data, with strong emphasis on the production of enriched graphical representation of the analysed data for the chromosome 21 genes.
- Links to the GeneClinics Database - a clinical information resource relating genetic testing to the diagnosis, management, and genetic counseling of individuals and families with specific inherited disorders.
- DOTS and MIPS assembly accession numbers are now sorted, with best matches displayed first.
- Since the last release, three new GeneCards mirror sites: in Turku, Finland at the Turku Centre for Biotechnology, in StonyBrook, NY, USA at the Medical Informatics Department, HSC, State University of NY at Stony Brook, and in Kowloon, Hong Kong at the Applied Research Centre for Genomic Technologies, City University of Hong Kong.
31 Jan 01: release of version 2.19
- 18,583 genes and 36 gene clusters, 11,980 of them with symbols approved by the HUGO gene nomenclature committee.
- Incorporation of UDB Version 2.0 data that integrates genomic contigs retrieved from NCBI (including finished and unfinished sequences) with the UDB map - SBR (Sequence-Based Repositioning)
- Comprehensive handling of aliased symbols. If there is more than 1 GeneCard for the requested alias, the links to all corresponding GeneCards are provided on a separate page (for example, RIP). This feature is applicable when the 'Search/Display GeneCards by symbol' option is chosen.
- Categorization of GeneCards into genes (e.g. BRCA1), clusters (e.g. IGLV@), disorder loci (e.g. PHA2A), pseudogenes (e.g. PROSP) or predicted genes (e.g. PRED26) in the GeneCard name box.
- Indication (by name box background color and descriptive text)
of data sources from which gene symbols were extracted. For example,
HUGO LocusLink MGD CroW 21
- Links to the Database of Human Unidentified Gene-Encoded Large Proteins - HUGE.
- More synonyms and aliases from GDB, HUGO, OMIM and SWISS-PROT.
- Since the last release, two new GeneCards mirror sites: in Canada at the Genome Sequence Centre, BC Cancer Agency, and in Tennessee, USA at the St. Jude Children's Research Hospital.
28 Nov 00: release of version 2.18
- 19,159 genes and 36 gene clusters, 11,688 of them with symbols approved by the HUGO gene nomenclature committee.
- Links to the University of California at Santa Cruz Human Draft Genomic Assembly .
- Links to the EuGene (Genomic Information for Eukaryotic Organisms) for more details on similar genes in other organisms.
- New section for links to other gene-based resources (GDB, LocusLink, EuGene).
- GenBank accession numbers for mouse homologs.
- Chromosomal location according to OMIM, UDB and LocusLink.
- A new GeneCards mirror site in Spain at The National Center for Oncology Research.
21 Sep 00: release of version 2.17
- 14169 genes, 11563 of them have gene symbols approved by the HUGO gene nomenclature committee.
- Cards for pseudogenes are now included.
- Additional information on Chromosome 21 locations from Nature 405, 311-319 and CroW 21/UDB.
- Links to the MIPS Pedant viewer for functional and structural characterization of protein sequences.
- Two new GeneCards mirror sites in Taiwan, at The Genome Research Center at The National Yang-Ming University , and at The Biomedical Engineering Center.
13 July 00: release of version 2.16
- 13147 genes, 10602 of them have gene symbols approved by the HUGO gene nomenclature committee.
- Improvements to the homepage:
- Capability to search UDB (The Unified Database for Human Genome Mapping)
- Capability to display an individual GeneCard based on its Hugo symbol
- Information on assemblies of sequences from DOTS the Database Of Transcribed Sequences, developed by the Computational Biology and Informatics Laboratory at the University of Pennsylvania.
- Links to entries in HORDE, the Human Olfactory Receptor Data Exploratorium at the Weizmann Institute of Science.
- Whole chromosome 21 sequence information from Nature 405, 311-319 and CroW, the Human Chromosome 21 Database at the Weizmann Institute of Science.
- Since the last release, two new GeneCards mirrors, at The Whitehead Institute for Biomedical Research, Cambridge, MA, USA, and at Duke Bioinformatics Shared Resource, Durham, NC, USA
15 May 00: release of version 2.15
- 10,286 genes, 10,047 of them have gene symbols approved by the HUGO gene nomenclature committee.
- Information on protein families from BLOCKS.
- Information on assemblies of sequences from MIPS.
- Additional links to OMIM.
- Improved display of sequences: definition of Unigene clusters, Unigene reresentative sequence, REFSEQ mRNAs, REFSEQ constructed genomic contigs, MIPS assemblies and Additional Gene/cDNA sequences.
- Improved display of GeneCard Disorder Information.
2 Mar. 00: release of version 2.14
- 9764 genes, 9521 of them have gene symbols approved by the HUGO gene nomenclature committee.
- More GenBank Accession Numbers even when no Unigene cluster exists.
- Minor bug fixes to the search engine
- Award from Britanica.com - GeneCards is a recommended site.
- SWISS-PROT links now point to their NiceProt user-friendly view.
- Updated Copyright notice , with link to fill-out form for commercial usage.
21 Dec. 99: release of version 2.13
- 9445 genes, 9191 of them have gene symbols approved by the HUGO gene nomenclature committee.
- Copyright notice .
- More disease information from Genatlas.
- Improved display: consolidation of disorders and mutations into one section. Moved HGMD, TGDB and BCGD from 'Additional Sources of Information' to 'Disorders & Mutations'. Renamed sections: 'Nucleic Acids' is now called 'Sequences'; 'Medical Applications' is now called 'Medical News'.
- Starting from November, two new GeneCards mirrors at the Imperial Cancer Research Fund, London, United Kingdom and at the Information Center, Beijing Medical University, Beijing, China.
3 Oct. 99: release of version 2.12
- 8968 genes, 8735 of them have gene symbols approved by the HUGO gene nomenclature committee.
- Links to Protein Data Bank (PDB) 3D structures; option to search by PDB identifier.
- A new GeneCards mirror at the Biological Research Information Center, Postech Pohany, South Korea.
18 July 99: release of version 2.11
- 8525 genes, 8395 of them have gene symbols approved by the HUGO gene nomenclature committee.
- Improved algorithm for linking to articles about medical applications in Doctor's Guide.
- Improved algorithm for locating OMIM information related to genes with ambigous aliases.
- A new GeneCards mirror at Italian EMBnet Node, Bari, Italy http://bio-www.ba.cnr.it:8000/GeneCards/
2 June 99: release of version 2.10
- 8455 genes, 8252 of them have gene symbols approved by the HUGO gene nomenclature committee.
- Improved algorithm for linking to articles about medical applications in Doctor's Guide.
- A link to the clone collection at the Resource center (RZPD), German Human Genome Project.
- Changes in format:
- A new GeneCards mirror at Stanford Genomic Resources, Stanford, CA, USA.
The left box of each field now links to the home pages of the data sources. The right columns present the retrieved data, and link to the relative entries in all the sources.
The "Disorders" field now presents disease data retrieved from SWISS-PROT in addition to the data retrieved from OMIM.
The "Similar Genes" field is displayed after the "Nucleic Acids" field.
Field boxes are presented even when they include no data, for a consistent format. A minor change in format of the HUGO approved gene symbol and name, in the top of the card.
8 April 99: release of version 2.9
- 8289 genes, 8099 of them have HUGO approved symbols.
- Map location: Distance (in megabases) from the p terminus of the chromosome as calculated by UDB, The Unified DataBase, linked to the map.
- Links to The Tumor Gene Database and to The Breast Cancer Gene Database.
- A new search option by chromosome: "chromosome: 3" in addition to the existing search by cytogenetic locus; e.g. "locus: 1q31", "locus: 1q3*".
- Changes in format: The section "Similar genes in other organisms" has been split to "Chromosomal location" (for chromosome, cytogenetic locus and map location) and "Similar genes in other organisms". Links to the Tumor and BreastCancer databases appear in the "Additional Sources of Information" field.
- A new GeneCards mirror at Centre for DNA Fingerprinting and Diagnostics, (CDFD), Hyderabad, India.
9 February 99: release of version 2.8
- 8105 genes, 7920 of them have HUGO approved symbols.
- New section of research articles with links to absracts in PubMed.
- Improved correlation between GeneCards and SWISS-PROT entries.
- A new GeneCards mirror in DKFZ in Germany.
9 December 98: Release of version 2.7
- 7853 genes, 7682 of them have HUGO approved symbols.
- Improved GeneCards correlation with UniGene clusters.
- New links to ATLAS.
- Changes in format:
- A new GeneCards mirror in The Netherlands, in addition to those in those in the USA and Turkey.
Nucleic Acid section appears earlier on the page.
Products section has been renamed "Proteins".
4 November 98: Release of version 2.6
- 7710 genes, 7541 of them have HUGO approved symbols.
- UniGene data is now displayed.
16 September 98: Release of version 2.5
- 7510 genes, 7344 of them have HUGO approved symbols.
- MGD descriptions are now displayed.
- Preliminary UniGene data has been added to the database but not yet displayed. Searches for GeneCards based on UniGene Hs. number, gene symbol or title, GenBank accession, EST's clone identifier or library ID are now possible.
22 July 98: Release of version 2.4 (7270 genes, 7098 of them have HUGO approved symbols).
10 Jun 98: Release of version 2.3.
- This release for the first time also includes genes that do not yet have an approved gene symbol, e.g. AOP1 and ART. These non-approved genes have been extracted from the Mouse Genome Database (MGD); they are very likely to become approved soon. On those GeneCards, a message is displayed on the top that indicates that this particular gene symbol and name are not approved.
- 7211 entries are offered (7062 have an approved gene symbol)
- Some smaller changes to the interface have been made (check the above cards)
- the SWISSPROT data field now also display the number of amino acids and the molecular weight
- the GeneCards access statistics page is richer, including numbers of accesses per day during the current month.
3 Jun 98: Release of version 2.2 (7022 genes).
13 May 98: Release of version 2.1 (7008 genes). Data from Genatlas are now included
1 Feb 98: Obtaining the GeneCards package for your site. Also included: a tour covering the main features of this resource.
25 Jan 98: The spell corrector now automatically offers suggestions for alternative spellings of keywords that do not occur in GeneCards. For example, try a search for Althshemer.
08 Dec 97: The GeneCards Web interface features a concept search, which is based on Excite for Web servers. For example, search for acetyl cholin esterase (note the link 'concept search')
12 Aug 97: An Introduction to HCI (Human-Computer Interaction) research, how it relates to the Web, and how its results are used for the design of the GeneCards Web interface, has been added.
06 Aug 97: The GeneCards search engine, whenever it returns some results, now also offers a link called 'More like this' that starts a search for other genes and proteins that have similar keywords in their names (for example, search for Alzheimer).
Also, the GeneCards display script is now highlighting your previously used search keywords in red, so it should be easier to find the lines that are interesting for you (for example, see how it looks like if you display the GeneCard for BRCA1 after searching for 'cancer AND ashkenazi').
Finally, you may find a new search button in every GeneCard that effectively retrieves useful information related to the gene/protein/disease on the Web, using Excite and a selection of keywords that appear in the GeneCard for searching. To find it, go to the GeneCard for APOE, scroll down (use the scrollbar on the right side of the browser window!), and look for the button called 'Search the WWW for APOE'.
21 Jul 97: As the Knowledge Navigation Guidance System is an important part of this resource, we have added another page to this server where you may find more information about it. Statistics about the different types of search problems that users have, and about the performance of the guidance system, will soon be published...
29 Jun 97: 39 new GeneCards have been added
hostname: 356980-web2.xennexinc.com index build: 128 solr: 1.4